Serial two-photon tomography for automated ex vivo mouse brain imaging

Ragan, Timothy; Kadiri, Lolahon; Venkataraju, Kannan Umadevi; Bahlmann, Karsten; Sutin, Jason; Taranda, Julián; Arganda‐Carreras, Ignacio; Kim, Yongsoo; Seung, H. Sebastian; Osten, Pavel

doi:10.1038/nmeth.1854

Cited by 631 publications

(639 citation statements)

References 34 publications

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“…Perfused and post-fixed brain from adult mice were embedded in oxidized agarose and imaged with TissueCyte 1000 (Tissuevision) as described before (Kim et al, 2015;Ragan et al, 2012).…”

Section: Stp Imagingmentioning

confidence: 99%

Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex

He¹,

Tucciarone²,

Lee³

et al. 2016

Neuron

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SummarySystematic genetic access to GABAergic cell types will facilitate studying the function and development of inhibitory circuitry. However, single gene-driven recombinase lines mark relatively broad and heterogeneous cell populations. Although intersectional approaches improve precision, it remains unclear whether they can capture cell types defined by multiple features. Here we demonstrate that combinatorial genetic and viral approaches target restricted GABAergic subpopulations and cell types characterized by distinct laminar location, morphology, axonal projection, and electrophysiological properties. Intersectional embryonic transcription factor drivers allow finer fate mapping of progenitor pools that give rise to distinct GABAergic populations, including laminar cohorts. Conversion of progenitor fate restriction signals to constitutive recombinase expression enables viral targeting of cell types based on their lineage and birth time. Properly designed intersection, subtraction, conversion, and multi-color reporters enhance the precision and versatility of drivers and viral vectors. These strategies and tools will facilitate studying GABAergic neurons throughout the mouse brain. eTOC BlurbHe et al. present strategies and tools for the combinatorial targeting of GABAergic neurons in the mouse brain. Specific cell type targeting can be achieved by combining 2 to 3 driver-reporter alleles with viral vectors that engage multiple cell-defining features.

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“…Perfused and post-fixed brain from adult mice were embedded in oxidized agarose and imaged with TissueCyte 1000 (Tissuevision) as described before (Kim et al, 2015;Ragan et al, 2012).…”

Section: Stp Imagingmentioning

confidence: 99%

Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex

He¹,

Tucciarone²,

Lee³

et al. 2016

Neuron

Self Cite

View full text Add to dashboard Cite

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“…However, light microscopy remains limited for imaging throughout intact vertebrate nervous systems (for example, mouse brains span many millimeters even in the shortest spatial dimension and are opaque on this scale, due chiefly to light scattering). A common work-around to this limitation has been to slice brains into thin sections, in manual or automated fashion, followed by confocal or two-photon imaging (Micheva et al 2010;Ragan et al 2012); however, detailed labeling and reconstruction from thin sections have been (so far) limited to small volumes of tissue. An ideal integrative approach would be to label and image entirely intact vertebrate brains at high resolution.…”

Section: Claritymentioning

confidence: 99%

Micro-, Meso- and Macro-Connectomics of the Brain

Kennedy¹,

Essen²,

Christen³

2016

Research and Perspectives in Neurosciences

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“…However, many commonly used methods ignore the additive term and directly normalize the observed image [2,5,9]. Our method, on the other hand, directly learns a mapping function from the true image to the observed image.…”

Section: Flat Field Correctionmentioning

confidence: 99%

“…Several approaches combine the normalization function with an additive term modeling the background [7,8]. Methods that correct the illumination of an image using only the normalization term [9] are only valid when the additive background term is zero. In most cases, modeling the background is necessary to properly correct the illumination level [6].…”

Section: Introductionmentioning

confidence: 99%

Vignetting and photo-bleaching correction in automated fluorescence microscopy from an array of overlapping images

Piccinini

Bevilacqua

Smith

et al. 2013

2013 IEEE 10th International Symposium on Biomedical Imaging

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We propose a novel acquisition scheme and non-parametric multi-image based method for correcting illumination in fluorescence images. Our approach measures changes in intensity of the subject by moving the microscope stage at regularly spaced intervals, and exploits this information to learn the correction function. The acquisition process and learning are performed prior to imaging, and take only a few minutes. Afterwards, images can be corrected for vignetting and photo-bleaching effects on the fly. Our approach can be implemented in any microscope with a motorized stage, and does not require a reference calibration slide. Experiments demonstrate that our method outperforms standard approaches to illumination correction. VIGNETTING AND PHOTO-BLEACHING CORRECTION IN AUTOMATED FLUORESCENCE MICROSCOPY FROM AN ARRAY OF OVERLAPPING IMAGES ABSTRACTWe propose a novel acquisition scheme and non-parametric multi-image based method for correcting illumination in fluorescence images. Our approach measures changes in intensity of the subject by moving the microscope stage at regularly spaced intervals, and exploits this information to learn the correction function. The acquisition process and learning are performed prior to imaging, and take only a few minutes. Afterwards, images can be corrected for vignetting and photobleaching effects on the fly. Our approach can be implemented in any microscope with a motorized stage, and does not require a reference calibration slide. Experiments demonstrate that our method outperforms standard approaches to illumination correction.

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Serial two-photon tomography for automated ex vivo mouse brain imaging

Cited by 631 publications

References 34 publications

Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex

Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex

Micro-, Meso- and Macro-Connectomics of the Brain

Vignetting and photo-bleaching correction in automated fluorescence microscopy from an array of overlapping images

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